Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ESR1

Cell type

Cell type Class
Breast
Cell type
Breast cancer cells
NA
NA

Attributes by original data submitter

Sample

source_name
Gar15-13 Decitabine tumour
tissue
Breast cancer PDX model Gar15-13
treatment
Decitabine
replicate
9
chip antibody
ER (Millipore SC-543X)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Samples snap-frozen in Optimal Cutting Temperature compound (Tissue-Tek) were used for ER and FOXA1 ChIP-seq experiments. Using a cryostat (Leica, #CM3050-S), 15x 30 µm sections were cut from each tumour at -20 ̊C and these samples were subjected to double fixation with DSG and formaldehyde as previously described (Singh et al., 2019). Library preparation for ChIP-Seq was performed using the QIAseq Ultralow Input Library Kit (Qiagen, #180495).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
30304994
Reads aligned (%)
96.8
Duplicates removed (%)
5.8
Number of peaks
8462 (qval < 1E-05)

hg19

Number of total reads
30304994
Reads aligned (%)
96.2
Duplicates removed (%)
6.8
Number of peaks
8364 (qval < 1E-05)

Base call quality data from DBCLS SRA